RetrogeneDB ID: retro_ecab_213

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: 10:21966444..21967212(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSECAG00000003274
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSECAG00000016162
• Aliases: None
• Description: None

Sequence

>retro_ecab_213
ATGGCTACCCAAAGGAAACACTTGGTAAAAGATTTCAATCCTTACATCACCTGCTATATCTGTAAAGGGTATCTGATCAA
GCCAACTACAGTGACCGAATGCCTCCATACCTTCTGTAAGACTTGTATTGTCCAGCACTTTGAAGATAGCAATGATTGTC
CAAGGTGTGGCAACCAGGTTCATGAGACCAATCCATTAGAAATGTTGAGGTTGGACAATACGTTAGAGGAAATCATATTT
AAACTGGTCCCTGGACTACGAGAACAAGAACTTGAGCGTGAATCTGAATTTTGGAAGAAAAATAAGCCTCGAGAAAATGG
ACAAGATGATACTTCAAAAGTTGACAGACCTAAAGTTGATGAAGAAGGTGATGAAAATCAAGATGATAAAGACTATCACA
GAAGTGACCCACAAATTGCTATATGTCTAGATTGTTTACGAAATAATGGACAATCAGGGGACAATGTAGTAAAGGGTTTA
ATGAAGAAATTCATTCGGTGTTCTACACGTGTAACTGTGGGAACTATTAAAAAATTTCTAAGTTTAAAACTAAAACTTCC
AAGTTCTTATGAGTTGGATGTGCTGTGCAATGGTGAAATTATGGGGAAGGATCATACTATGGAATTCATCTACATGACGA
GGTGGCGACTAAGAGGCGAAAACTTTCGGTGTCTGAACTGCTCAGCTTCGCAAGTCTGCTCTCAGGATGGCCCTTTATAT
CAGTCATACCCCATGGTATTGCAGTATCGACCGAGAATTGATTTTGGT

Alignment

ORF - retro_ecab_213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.48 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATQRKHLVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQLMTTPFFQLLR
          MATQRKHLVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQ...T.....LR
Retrocopy MATQRKHLVKDFNPYITCYICKGYLIKPTTVTECLHTFCKTCIVQHFEDSNDCPRCGNQVHETNPLEMLR

Parental  LDNTLEEIIFKLVPGLREQELERESEFWKKNKPQENGQDDTSKVDRPKVDEEGDENQDDKDYHRSDPQIA
          LDNTLEEIIFKLVPGLREQELERESEFWKKNKP.ENGQDDTSKVDRPKVDEEGDENQDDKDYHRSDPQIA
Retrocopy LDNTLEEIIFKLVPGLREQELERESEFWKKNKPRENGQDDTSKVDRPKVDEEGDENQDDKDYHRSDPQIA

Parental  ICLDCLRNNGQSGDNVVKGLMKKFIRCSTRVTVGTIKKFLSLKLKLPSSYELDVLCNGEIMGKDHTMEFI
          ICLDCLRNNGQSGDNVVKGLMKKFIRCSTRVTVGTIKKFLSLKLKLPSSYELDVLCNGEIMGKDHTMEFI
Retrocopy ICLDCLRNNGQSGDNVVKGLMKKFIRCSTRVTVGTIKKFLSLKLKLPSSYELDVLCNGEIMGKDHTMEFI

Parental  YMTRWRLRGENFRCLNCSASQVCSQDGPLYQSYPMVLQYRPRIDFG
          YMTRWRLRGENFRCLNCSASQVCSQDGPLYQSYPMVLQYRPRIDFG
Retrocopy YMTRWRLRGENFRCLNCSASQVCSQDGPLYQSYPMVLQYRPRIDFG

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP021940_articular_cartilage	0.30 RPM	4.60 RPM
SRP021940_cerebellum	0.05 RPM	0.57 RPM
SRP021940_embryo	0.08 RPM	1.53 RPM
SRP021940_placental_villous	0.10 RPM	4.14 RPM
SRP021940_synovial_membrane	0.05 RPM	1.35 RPM
SRP021940_testis	0.70 RPM	10.04 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_213 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_213 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_213 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011001	1 retrocopy	retro_cjac_2702,
Equus caballus	ENSECAG00000016162	1 retrocopy	retro_ecab_213 ,
Microcebus murinus	ENSMICG00000012035	5 retrocopies	retro_mmur_1358, retro_mmur_1499, retro_mmur_253, retro_mmur_858, retro_mmur_982,
Procavia capensis	ENSPCAG00000007871	1 retrocopy	retro_pcap_302,
Ictidomys tridecemlineatus	ENSSTOG00000009179	1 retrocopy	retro_itri_1546,
Tursiops truncatus	ENSTTRG00000014814	1 retrocopy	retro_ttru_1529,